The UK government says an independent Scotland would have to apply as a new member state to join the European Union, with uncertain consequences.

In a brief statement issued on Thursday, Westminster hinted strongly that its legal advice directly contradicted the claim by Scotland's first minister, Alex Salmond, that, if Scotland voted for independence, it and the rest of the UK would need to reapply to join the EU as newly formed states.

As the controversy over Salmond's stance on Europe again dominated first minister's questions at Holyrood, the UK government said its position was that only Scotland would have to apply to join as a new state if voters chose independence in 2014.

Separately, in a speech on Europe to the Royal Institute of International Affairs at Chatham House in London, the deputy prime minister Nick Clegg entered the fray, stating that Salmond's statements on Scotland getting automatic membership of the EU "has no basis in fact".

He said Scottish nationalists "don't want to face what might happen to Scotland's influence on fishing quotas, or agricultural policy, or the regulation of the banks. They don't want reality to bite. So they've gone into denial, preferring political assertion to legal advice."

The dispute has suddenly dominated the debate about the Scottish independence referendum after Salmond's deputy, Nicola Sturgeon, revealed last week that the Scottish National party government had not sought its own legal advice on EU membership, despite statements by Salmond that it had.

The UK government statement stressed that, unlike the Scottish government, it had obtained formal advice from its law officers and that Scotland would have to negotiate the terms of its EU membership with the UK and all other 26 member states.

It said: "This government has confirmed it does hold legal advice on this issue. Based on the overwhelming weight of international precedent, it is the government's view that the remainder of the UK would continue to exercise the UK's existing international rights and obligations and Scotland would form a new state.

"The most likely scenario is that the rest of the UK would be recognised as the continuing state and an independent Scotland would have to apply to join the EU as a new state, involving negotiation with the rest of the UK and other member states, the outcome of which cannot be predicted."

Referring to statements by European commission president, José Manuel Barroso, and his deputy, Viviane Reding, that a newly independent country would be seen as a new applicant, it added: "Recent pronouncements from the commission support that view."

It rejected Salmond's suggestion that the UK should take up the commission's offer to provide any member state with a clear view on the membership rights of a newly-formed state within the EU.

The commission has recently said that after the deal between Salmond and David Cameron to stage the independence referendum, known as the Edinburgh agreement, it could offer its opinion if a member state provided a detailed and specific scenario.

Officials said Salmond had not actually officially asked the UK government to do so, and added that it was the Scottish government's problem, not the UK's.

"The UK government does not obtain its legal advice from the European commission," the statement from Westminster said. "We are clear that we are not pre-negotiating the terms of separation from the UK ahead of the referendum. It is the Scottish government's policy on independence which is causing this uncertainty and they should be prepared to deal with the many questions it raises."

Salmond was goaded during first minister's questions about the controversy that erupted last week and escalated further after Spain's foreign minister, José Manuel García-Margallo, said an independent Scotland would have to "join the queue" for EU membership.

Johann Lamont, the Scottish Labour leader, said the first minister was "treating the people of Scotland like fools" and was no longer trusted to tell the truth. "What is it that he's so scared of, that he can't ask the Bank of England about the pound; he can't ask other EU members about Europe?" she asked.

Salmond retaliated by quoting from an expert on the EU's borders, Graham Avery, a former strategy director at the commission who was made one of a number of honorary directors general of the European commission after he retired.

In a submission to the Commons foreign affairs select committee, Avery supported Salmond's position that it was inconceivable that an independent Scotland would be expected to leave the EU and then reapply. Salmond said his opinion "rather puts the lie to the scaremongering campaign of Labour and their unionist colleagues in the Conservative party".

"For practical and political reasons, they could not be asked to leave the EU and apply for readmission," Avery told the committee. "Negotiations on the terms of membership would take place in the period between the referendum and the planned date of independence. The EU would adopt a simplified procedure for the negotiations, not the traditional procedure followed for the accession of non-member countries."

But Avery, now at St Antony's College, Oxford University, directly contradicted Salmond's assertions that an independent Scotland would not be expected to join the euro instead of sterling, and that it would not need to sign up to the Schengen agreement rules on security and immigration.

Avery said independence would give Scotland a louder and stronger voice in the EU, but new member states "are required to accept [the euro and Schengen] on principle". While Scotland's position was still not clear, Avery warned: "In accession negotiations with non-member countries, the EU has always strongly resisted other changes or opt-outs from the basic treaties."

• This article was amended on 2 November 2012. The original referred to a speech on Europe to the Royal United Services Institute, rather than the Royal Institute of International Affairs, at Chatham House in London. This has been corrected.